The soldier was shot dead at a checkpoint in the town, capital of Lahij province, a security source said.
Tensions have run high in Huta since a wave of arrests targeting suspected Al-Qaeda militants prompted a Sunday assault on the police station where they were being held, killing a soldier.
Lahij province is home to the Al-Anad air base, north of the main southern city of Aden, where Yemeni officials have said Washington has personnel deployed gathering intelligence for its drone war against Al-Qaeda.
Commanders say they have killed more than 500 militants, but the jihadists have regrouped in the mountains and in neighbouring provinces.
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A suspected Al-Qaeda gunman killed a civilian in Huta yesterday.
Al-Qaeda took advantage of the collapse of central authority during a 2011 uprising that forced veteran strongman Ali Abdullah Saleh from power to seize large swathes of the south and east.
The jihadists remain deeply entrenched in Hadramawt province farther east where they have carried out a series of spectacular attacks in recent months.